data_6Y8K # _model_server_result.job_id x_qzSRKGj2TlULVU-7HiKQ _model_server_result.datetime_utc '2024-10-12 07:27:24' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6y8k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":101}' # _entry.id 6Y8K # _exptl.entry_id 6Y8K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 255.313 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6Y8K _cell.length_a 122.47 _cell.length_b 122.47 _cell.length_c 122.47 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y8K _symmetry.cell_setting ? _symmetry.Int_Tables_number 208 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 25 AAA CYS 28 1_555 A SG CYS 34 AAA CYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf2 A SG CYS 28 AAA CYS 31 1_555 A SG CYS 42 AAA CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf3 A SG CYS 45 AAA CYS 48 1_555 A SG CYS 59 AAA CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? disulf ? disulf4 A SG CYS 62 AAA CYS 65 1_555 A SG CYS 75 AAA CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 A SG CYS 65 AAA CYS 68 1_555 A SG CYS 83 AAA CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 85 AAA CYS 88 1_555 A SG CYS 99 AAA CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf7 A SG CYS 91 AAA CYS 94 1_555 A SG CYS 96 AAA CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 A SG CYS 103 AAA CYS 106 1_555 A SG CYS 114 AAA CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf9 A SG CYS 117 AAA CYS 120 1_555 A SG CYS 130 AAA CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 A SG CYS 136 AAA CYS 139 1_555 A SG CYS 155 AAA CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 B SG CYS 1 PPP CYS 1 1_555 I C19 29N . PPP 29N 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? covale ? covale2 B SG CYS 8 PPP CYS 8 1_555 I C16 29N . PPP 29N 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? covale ? covale3 B C TYR 13 PPP TYR 13 1_555 B N NLE 14 PPP NLE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale4 B C NLE 14 PPP NLE 14 1_555 B N CYS 15 PPP CYS 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale5 B SG CYS 15 PPP CYS 15 1_555 I C25 29N . PPP 29N 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.656 ? # _chem_comp.formula 'C12 H21 N3 O3' _chem_comp.formula_weight 255.313 _chem_comp.id 29N _chem_comp.mon_nstd_flag . _chem_comp.name "1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C25 C14 29N sing 1 n n O15 C13 29N doub 2 n n C14 C13 29N sing 3 n n C13 N3 29N sing 4 n n C16 C8 29N sing 5 n n C8 C7 29N sing 6 n n N3 C2 29N sing 7 n n N3 C4 29N sing 8 n n C2 N1 29N sing 9 n n C7 N1 29N sing 10 n n C7 O9 29N doub 11 n n N1 C6 29N sing 12 n n C4 N5 29N sing 13 n n C19 C11 29N sing 14 n n N5 C6 29N sing 15 n n N5 C10 29N sing 16 n n C11 C10 29N sing 17 n n C10 O12 29N doub 18 n n C2 H1 29N sing 19 n n C2 H2 29N sing 20 n n C4 H3 29N sing 21 n n C4 H4 29N sing 22 n n C6 H5 29N sing 23 n n C6 H6 29N sing 24 n n C8 H7 29N sing 25 n n C8 H8 29N sing 26 n n C11 H9 29N sing 27 n n C11 H10 29N sing 28 n n C14 H11 29N sing 29 n n C14 H12 29N sing 30 n n C16 H13 29N sing 31 n n C16 H14 29N sing 32 n n C16 H15 29N sing 33 n n C19 H16 29N sing 34 n n C19 H17 29N sing 35 n n C19 H18 29N sing 36 n n C25 H19 29N sing 37 n n C25 H20 29N sing 38 n n C25 H21 29N sing 39 n n # _atom_sites.entry_id 6Y8K _atom_sites.fract_transf_matrix[1][1] 0.008165 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008165 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008165 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 ACT AAA 1 201 201 ACT ACT . D 4 EDO AAA 1 202 202 EDO EDO . E 5 SO4 AAA 1 203 203 SO4 SO4 . F 5 SO4 AAA 1 204 204 SO4 SO4 . G 5 SO4 AAA 1 205 205 SO4 SO4 . H 6 NA AAA 1 206 206 NA NA . I 7 29N PPP 1 101 101 29N TA9 . J 8 HOH AAA 1 301 2 HOH HOH . J 8 HOH AAA 2 302 22 HOH HOH . J 8 HOH AAA 3 303 19 HOH HOH . J 8 HOH AAA 4 304 7 HOH HOH . J 8 HOH AAA 5 305 13 HOH HOH . J 8 HOH AAA 6 306 12 HOH HOH . J 8 HOH AAA 7 307 8 HOH HOH . J 8 HOH AAA 8 308 23 HOH HOH . J 8 HOH AAA 9 309 24 HOH HOH . J 8 HOH AAA 10 310 15 HOH HOH . J 8 HOH AAA 11 311 28 HOH HOH . J 8 HOH AAA 12 312 9 HOH HOH . J 8 HOH AAA 13 313 27 HOH HOH . J 8 HOH AAA 14 314 20 HOH HOH . J 8 HOH AAA 15 315 25 HOH HOH . J 8 HOH AAA 16 316 3 HOH HOH . J 8 HOH AAA 17 317 14 HOH HOH . J 8 HOH AAA 18 318 16 HOH HOH . J 8 HOH AAA 19 319 4 HOH HOH . J 8 HOH AAA 20 320 18 HOH HOH . J 8 HOH AAA 21 321 5 HOH HOH . J 8 HOH AAA 22 322 10 HOH HOH . J 8 HOH AAA 23 323 30 HOH HOH . J 8 HOH AAA 24 324 1 HOH HOH . J 8 HOH AAA 25 325 11 HOH HOH . J 8 HOH AAA 26 326 17 HOH HOH . J 8 HOH AAA 27 327 6 HOH HOH . J 8 HOH AAA 28 328 29 HOH HOH . K 8 HOH PPP 1 201 21 HOH HOH . K 8 HOH PPP 2 202 26 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 29N . . . I 7 39.911 -4.625 -36.636 1 69.38 ? N1 29N 101 PPP 1 HETATM 2 C C2 29N . . . I 7 39.611 -5.209 -37.941 1 64.26 ? C2 29N 101 PPP 1 HETATM 3 N N3 29N . . . I 7 40.37 -4.364 -38.855 1 65.97 ? N3 29N 101 PPP 1 HETATM 4 C C4 29N . . . I 7 41.815 -4.51 -38.606 1 72.67 ? C4 29N 101 PPP 1 HETATM 5 N N5 29N . . . I 7 42.089 -3.92 -37.289 1 61.1 ? N5 29N 101 PPP 1 HETATM 6 C C6 29N . . . I 7 41.349 -4.71 -36.309 1 64.42 ? C6 29N 101 PPP 1 HETATM 7 C C7 29N . . . I 7 38.979 -4.009 -35.88 1 65.08 ? C7 29N 101 PPP 1 HETATM 8 C C8 29N . . . I 7 39.418 -3.325 -34.615 1 64.01 ? C8 29N 101 PPP 1 HETATM 9 O O9 29N . . . I 7 37.809 -3.973 -36.227 1 61.33 ? O9 29N 101 PPP 1 HETATM 10 C C10 29N . . . I 7 42.768 -2.773 -37.093 1 60.53 ? C10 29N 101 PPP 1 HETATM 11 C C11 29N . . . I 7 42.845 -2.165 -35.721 1 67.98 ? C11 29N 101 PPP 1 HETATM 12 O O12 29N . . . I 7 43.285 -2.179 -38.025 1 63.31 ? O12 29N 101 PPP 1 HETATM 13 C C13 29N . . . I 7 39.878 -3.434 -39.692 1 72.03 ? C13 29N 101 PPP 1 HETATM 14 C C14 29N . . . I 7 38.364 -3.297 -39.8 1 72.38 ? C14 29N 101 PPP 1 HETATM 15 O O15 29N . . . I 7 40.657 -2.711 -40.3 1 66.22 ? O15 29N 101 PPP 1 HETATM 16 C C16 29N . . . I 7 38.3 -2.625 -33.858 1 60.39 ? C16 29N 101 PPP 1 HETATM 17 C C19 29N . . . I 7 44.202 -1.551 -35.403 1 71.48 ? C19 29N 101 PPP 1 HETATM 18 C C25 29N . . . I 7 37.79 -2.088 -40.531 1 80.81 ? C25 29N 101 PPP 1 HETATM 19 H H1 29N . . . I 7 38.665 -5.171 -38.101 1 64.26 ? H1 29N 101 PPP 1 HETATM 20 H H2 29N . . . I 7 39.9 -6.124 -37.958 1 64.26 ? H2 29N 101 PPP 1 HETATM 21 H H3 29N . . . I 7 42.065 -5.437 -38.602 1 72.67 ? H3 29N 101 PPP 1 HETATM 22 H H4 29N . . . I 7 42.321 -4.047 -39.278 1 72.67 ? H4 29N 101 PPP 1 HETATM 23 H H5 29N . . . I 7 41.507 -4.361 -35.429 1 64.42 ? H5 29N 101 PPP 1 HETATM 24 H H6 29N . . . I 7 41.641 -5.624 -36.346 1 64.42 ? H6 29N 101 PPP 1 HETATM 25 H H7 29N . . . I 7 40.11 -2.665 -34.83 1 64.01 ? H7 29N 101 PPP 1 HETATM 26 H H8 29N . . . I 7 39.832 -3.985 -34.02 1 64.01 ? H8 29N 101 PPP 1 HETATM 27 H H9 29N . . . I 7 42.155 -1.475 -35.636 1 67.98 ? H9 29N 101 PPP 1 HETATM 28 H H10 29N . . . I 7 42.641 -2.852 -35.053 1 67.98 ? H10 29N 101 PPP 1 HETATM 29 H H11 29N . . . I 7 37.98 -3.253 -38.899 1 72.38 ? H11 29N 101 PPP 1 HETATM 30 H H12 29N . . . I 7 38.004 -4.074 -40.276 1 72.38 ? H12 29N 101 PPP 1 HETATM 31 H H13 29N . . . I 7 37.64 -3.285 -33.559 1 60.39 ? H13 29N 101 PPP 1 HETATM 32 H H14 29N . . . I 7 37.931 -1.903 -34.408 1 60.39 ? H14 29N 101 PPP 1 HETATM 33 H H16 29N . . . I 7 44.38 -0.807 -36.015 1 71.48 ? H16 29N 101 PPP 1 HETATM 34 H H17 29N . . . I 7 44.889 -2.25 -35.405 1 71.48 ? H17 29N 101 PPP 1 HETATM 35 H H19 29N . . . I 7 38.063 -2.111 -41.472 1 80.81 ? H19 29N 101 PPP 1 HETATM 36 H H20 29N . . . I 7 38.038 -1.267 -40.057 1 80.81 ? H20 29N 101 PPP 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #